COL2A1 T9S - GET-Evidence

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Note: This variant has not been sufficiently evaluated by a GET-Evidence editor.

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Curation:
Currentness:

COL2A1 T9S

(COL2A1 Thr9Ser)


Short summary

 

Variant evidence
Computational 3

PolyPhen2: Unknown
SIFT: Affect protein function 0.00
GVGD: GV 0.00; GD 57.75; Class C55
Variant Effect Predictor (Ensembl):
SIFT=tolerated(0.73);
PolyPhen=unknown(0)
Mutation Tasting Prediction: Polymorphism, P value: 0.952409; protein features (might be) affected (aa 1-25 SIGNAL Potential gets lost)

Functional -
Case/Control -
Familial -
 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Insufficiently evaluated not reviewed

(The "insufficiently evaluated" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

unknown

Summary of published research, and additional commentary

 

Allele frequency

  • A @ chr12:48398080: 79.1% (7201/9106) in EVS
  • A @ chr12:46684346: 70.0% (28/40) in GET-Evidence
  • Frequency shown in summary reports: 79.1% (7201/9106)

Publications
 

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
hom A @ chr12:48398080

 

hu0E64A1 - CGI sample GS01173-DNA_B02 from PGP sample 94378523
hom A @ chr12:48398080

 

hu232307 - PGP14 (hu232307) build 36, substitution variants, hu232307 build 36 substitution variants
hom A @ chr12:46684347

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
hom A @ chr12:48398080

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
het A @ chr12:48398080

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
hom A @ chr12:48398080

 

hu3215A7 - PGP12 (hu3215A7) build 36, substitution variants, hu3215A7 build 36 substitution variants
het A @ chr12:46684347

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
het A @ chr12:48398080

 

hu34D5B9 - CGI sample GS01173-DNA_C07 from PGP sample 92161424
hom A @ chr12:48398080

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
het A @ chr12:48398080

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
hom A @ chr12:48398080

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
hom A @ chr12:48398080

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
hom A @ chr12:48398080

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
hom A @ chr12:48398080

 

hu4CA5B9 - CGI sample GS01669-DNA_B03 from PGP sample 14427241
hom A @ chr12:48398080

 

hu728FFF - PGP11 (hu728FFF) build 36, substitution variants, hu728FFF build 36 substitution variants
hom A @ chr12:46684347

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
hom A @ chr12:48398080

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
hom A @ chr12:48398080

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het A @ chr12:48398080

 

hu92FD55 - CGI sample GS01669-DNA_A04 from PGP sample 08188426
hom A @ chr12:48398080

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
hom A @ chr12:48398080

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
hom A @ chr12:48398080

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
hom A @ chr12:48398080

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het A @ chr12:48398080

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
hom A @ chr12:48398080

 

huD37D14 - CGI sample GS01175-DNA_A04 from PGP sample 13272228
het A @ chr12:48398080

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
het A @ chr12:48398080

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het A @ chr12:48398080

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
het A @ chr12:48398080

 

GS07357 - var-GS07357-1100-36-ASM
hom A @ chr12:46684347

 

GS12004 - var-GS12004-1100-36-ASM
hom A @ chr12:46684347

 

GS18526 - var-GS18526-1100-36-ASM
hom A @ chr12:46684347

 

GS18555 - var-GS18555-1100-36-ASM
het A @ chr12:46684347

 

GS18940 - var-GS18940-1100-36-ASM
hom A @ chr12:46684347

 

GS18956 - var-GS18956-1100-36-ASM
het A @ chr12:46684347

 

GS19017 - var-GS19017-1100-36-ASM
hom A @ chr12:46684347

 

GS19129 - var-GS19129-1100-36-ASM
hom A @ chr12:46684347

 

GS19834 - var-GS19834-1100-36-ASM
hom A @ chr12:46684347

 

GS20509 - var-GS20509-1100-36-ASM
het A @ chr12:46684347

 

GS21767 - var-GS21767-1100-36-ASM
hom A @ chr12:46684347

 

NA19240

 

Other external references
 

    dbSNP
  • rs3803183
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the COL2A1 gene
    Stickler Syndrome
    Achondrogenesis Type 2
    Avascular Necrosis of Femoral Head, Primary
    COL2A1-Associated Stickler Syndrome
    COL2A1-Related Stickler Syndrome
    Kniest Dysplasia
    Osteoarthritis with Mild Chondrodysplasia
    Platyspondylic Lethal Skeletal Dysplasia, Torrance Type
    Spondyloepimetaphyseal Dysplasia, Strudwick Type
    Spondyloepiphyseal Dysplasia
    Spondyloepiphyseal Dysplasia, Congenita
    Spondyloperipheral Dysplasia
    Type II Collagenopathies
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL2A1

Other in silico analyses
 

  • NBLOSUM100 score = –2
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

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